1 files changed, 87 insertions, 0 deletions
diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
new file mode 100755
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+++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+
+import gudhi
+import sys
+import argparse
+
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+    Author(s):       Vincent Rouvreau
+
+    Copyright (C) 2017 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 Inria"
+__license__ = "MIT"
+
+parser = argparse.ArgumentParser(
+    description="RipsComplex creation from " "a correlation matrix read in a csv file.",
+    epilog="Example: "
+    "example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py "
+    "-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3"
+    "- Constructs a Rips complex with the "
+    "correlation matrix from the given csv file.",
+)
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band", type=float, default=0.0)
+parser.add_argument(
+    "--no-diagram",
+    default=False,
+    action="store_true",
+    help="Flag for not to display the diagrams",
+)
+
+args = parser.parse_args()
+
+if not (-1.0 < args.min_edge_correlation < 1.0):
+    print("Wrong value of the treshold corelation (should be between -1 and 1).")
+    sys.exit(1)
+
+print("#####################################################################")
+print("Caution: as persistence diagrams points will be under the diagonal,")
+print("bottleneck distance and persistence graphical tool will not work")
+print("properly, this is a known issue.")
+
+print("#####################################################################")
+print("RipsComplex creation from correlation matrix read in a csv file")
+
+message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation)
+print(message)
+
+correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
+    csv_file=args.file
+)
+# Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
+distance_matrix = [
+    [1.0 - correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))]
+    for i in range(len(correlation_matrix))
+]
+
+rips_complex = gudhi.RipsComplex(
+    distance_matrix=distance_matrix, max_edge_length=1.0 - args.min_edge_correlation
+)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence()
+
+print("betti_numbers()=")
+print(simplex_tree.betti_numbers())
+
+# invert the persistence diagram
+invert_diag = [
+    (diag[pers][0], (1.0 - diag[pers][1][0], 1.0 - diag[pers][1][1]))
+    for pers in range(len(diag))
+]
+
+if args.no_diagram == False:
+    pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band)
+    pplot.show()